2XTJA

The crystal structure of pcsk9 in complex with 1d05 fab
Warning
  • Chain breaks within knot 31 (displayed as a gray area on the plot and as '-' on the sequence). The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Genus: 83
Slipknot S +31

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Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
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+31 29-99 71 1-28 102-268 100-101 28 167 slipknot
Chain Sequence
PWN--------------------SLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDQASKCDSHGTHLAGVVSGRD------AGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLILFSAKD
Whole chain analysis

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Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1


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Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
view details
2.1 10-69 60 1-9 78-242 70-77 9 165 slipknot
view details
1.1 15-70 56 1-9, 78-242 10-14, 71-77 9 165 slipknot
sequence length 268
structure length 242
publication title A Pcsk9-Binding Antibody that Structurally Mimics the Egf(A) Domain of Ldl-Receptor Reduces Ldl Cholesterol in Vivo.
pubmed doi rcsb
molecule tags Hydrolase/antibody
molecule keywords PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
source organism Homo sapiens
missing residues 4-23, 59-64
total genus Genus: 83
ec nomenclature ec 3.4.21.-:
pdb deposition date 2010-10-10
KnotProt deposition date 2014-07-31

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00082 Peptidase_S8 Subtilase family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.50.200 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Rossmann fold 2xtjA00
1DBIA 2XTJA
chains in the KnotProt database with same CATH superfamily
1E2JA 1KI6B 3VTKA 1II9A 1KI8A 3M4NA 4IVRA 1QHIA 3F0TA 1P7CA 3L05A 3L06A 1YVEI 1E2PA 1KI6A 1R4MB 4JBXA 3KZMA 1E2HA 1DBIA 1E2NA 1F48A 1E2LA 2KI5A 1E2KA 1P75A 1YH1A 4IVPA 1LNSA 1P6XA 3KZKA 3RDPA 1KI7A 3KZCA 3M5CA 1JS1X 4IVQA 1KIMA 1KI2A 1OF1A 2VTKA 2XTJA 1P72A 1P73A 1E2MA 3M4JA 1GKUB 3L04A 3FR7A 1E2IA 1KI4A 3KZOA 1YRLA 3FR8A 4JBYA 3M5DA 1OSNA 3L02A 1R4NB 2FG6C 1QMGA 3KZNA 1KI3A 2G7MC 3FSGA 1VTKA
chains in the KnotProt database with same CATH topology
3M4NA 3L05A 3L06A 3KZMA 1DBIA 1YH1A 1LNSA 3KZKA 3KZCA 3M5CA 1JS1X 2XTJA 3M4JA 1GKUB 3L04A 3KZOA 3L02A 2FG6C 3KZNA 2G7MC 3FSGA 3M5DA
chains in the KnotProt database with same CATH homology

  
#chains in the KnotProt database with same CATH superfamily
 1DBI A;  2XTJ A; 
#chains in the KnotProt database with same CATH topology
 1E2J A;  1KI6 B;  3VTK A;  1II9 A;  1KI8 A;  3M4N A;  4IVR A;  1QHI A;  3F0T A;  1P7C A;  3L05 A;  3L06 A;  1YVE I;  1E2P A;  1KI6 A;  1R4M B;  4JBX A;  3KZM A;  1E2H A;  1DBI A;  1E2N A;  1F48 A;  1E2L A;  2KI5 A;  1E2K A;  1P75 A;  1YH1 A;  4IVP A;  1LNS A;  1P6X A;  3KZK A;  3RDP A;  1KI7 A;  3KZC A;  3M5C A;  1JS1 X;  4IVQ A;  1KIM A;  1KI2 A;  1OF1 A;  2VTK A;  2XTJ A;  1P72 A;  1P73 A;  1E2M A;  3M4J A;  1GKU B;  3L04 A;  3FR7 A;  1E2I A;  1KI4 A;  3KZO A;  1YRL A;  3FR8 A;  4JBY A;  3M5D A;  1OSN A;  3L02 A;  1R4N B;  2FG6 C;  1QMG A;  3KZN A;  1KI3 A;  2G7M C;  3FSG A;  1VTK A; 
#chains in the KnotProt database with same CATH homology
 3M4N A;  3L05 A;  3L06 A;  3KZM A;  1DBI A;  1YH1 A;  1LNS A;  3KZK A;  3KZC A;  3M5C A;  1JS1 X;  2XTJ A;  3M4J A;  1GKU B;  3L04 A;  3KZO A;  3L02 A;  2FG6 C;  3KZN A;  2G7M C;  3FSG A;  3M5D A;
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similar chains in the KnotProt database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

  
#similar chains in the KnotProt database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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How to cite
KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling